The scenario you describe where a player needed to think about what stacked with what almost never occurred. It was very simple then because the number of ways to get a bonus that could stack were extremely low and they rarely were able to stack with themselves if you happened to find a way that you could double up on a particular bonus. Even beyond that there were few ways to get anything but armor shield or enhancement bonus.
If anything, Pathfinder 1e was where situational bonuses really got out of hand. Just looking at my Oracle, she has:
+2 AC vs. critical hit confirmation rolls.
+2 dodge bonus to AC in cold environments.
+2 on saves vs. charms and compulsions.
+4 on Will saves vs. fear.
+2 competence bonus for Will mind-affecting saves.
+3 to Will mind-affecting saves.
+5 circumstance bonus to Bluff and Diplomacy checks when dealing with individuals who might find her attractive.
-10 penalty to Will saves made against non-mind-affecting Divination spells and spell-like abilities.
+1 to hit with Opportunity attacks.
+Cha mod to healing received from others.
The save bonuses alone slow down play immensely, as I constantly have to ask if a given Will save is mind-affecting or a charm/compulsion, and of course, monster abilities in Pathfinder 1e will often lack sufficient keywords to inform you, so the GM has to make a call every time.
By contrast, I can look at my 3.5 Cleric and see that while he has many bonuses (he uses Divine Metamagic to tag the entire party with 24-hour buffs and then mostly heals or uses his Reserve Feat while letting the rest of the party wreck encounters), they're all quite straightforward, increasing AC, saves, attacks, or skills. Calculating touch AC is fairly easy- just ignore armor and natural armor, everything else counts. Calculating flat-footed AC is also fairly easy- ignore Dexterity and Dodge bonuses.
That having been said, even with me handing out note cards to the other players with their party buffs active, some of the players would still somehow forget that they had a +2 sacred bonus on attack and damage rolls, which confused me when these were the same guys constantly jockeying to get flanking bonuses.
Eventually the DM solved this problem by giving everyone fillable pdf character sheets with boxes you could check that would instantly update your sheet with all the modifiers, lol.